Hi Carmen,
not sure if that might be the cause, but does your input pdb contain water
hydrogens? Does your output look better when you delete them and have leap
re-add them to your system? I would normally expect X-ray crystal waters
to only have the oxygen position resolved, but I dont know where your pdb
comes from...
Regards,
Thomas
On Mon, January 12, 2009 3:04 pm, Carmen Domene wrote:
>
> Hi.
>
> I have been checking in the amber repository but I have not found a
> solution to my problem. I am trying to generate the topology file for a
> system composed of a protein, a ligand and some crystal waters. I would
> also like to solvate it and add counter ions.
>
> I am using this set of commands:
>
> tleap -s -f leaprc.ff99SB
> source leaprc.gaff
> loadamberprep p.prepin
> loadamberparams p.frcmod
> LIG=loadpdb all_1.pdb
> check LIG
> solvateBOX LIG TIP3PBOX 11
> addions LIG Na+ 0
> center LIG
> >The center is at: 0.27, 0.14, -0.09
> translate LIG {-0.27, -0.14, 0.09}
> center LIG
> >The center is at: 0.00, -0.00, -0.00
> savepdb LIG all_c.pdb
> LIG2=loadpdb all_c.pdb
> saveamberparm LIG2 all_c.prmtop all_c.inpcrd
>
> I am using Amber9.
>
>
> What I find is that the crystal waters and the waters
> added by the solvation procedure have the atoms organised
> in different ways, for example 832 is a crystal water
> and 833 is a water added during solvation:
>
> TER
> ATOM 7774 H1 WAT 832 -32.473 -7.620 7.472 1.00 0.00
> ATOM 7775 H2 WAT 832 -33.670 -6.694 7.472 1.00 0.00
> ATOM 7776 O WAT 832 -33.430 -7.620 7.472 1.00 0.00
> TER
> ATOM 7777 O WAT 833 41.569 48.050 38.824 1.00 0.00
> ATOM 7778 H1 WAT 833 40.737 47.794 39.224 1.00 0.00
> ATOM 7779 H2 WAT 833 42.177 48.121 39.560 1.00 0.00
> TER
>
> When I run the MD I can see the crystal waters look wrong with d_O-H1
> different from d_O-H2.
>
> What should I do to have the atoms in the same order in all the water
> molecules?
>
> I have tried using HOH rather than WAT or the other way round. Adding
> 'TER' after each O of the crystal waters...
>
> Thanks,
>
> Carmen
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Wed Jan 14 2009 - 01:13:46 PST
